NAMD Utilities
Related Packages
- VMD
(with its plugins and
script library)
is closely tied to NAMD and is used for:
- visualizing the initial structure and trajectory
- assembling biomolecular aggregates
- solvating the system in a membrane and/or water
- building the molecular structure (PSF file)
- visualizing and analyzing the trajectory
- Tcl is used within NAMD and VMD to provide scripting capabilities.
- FFTW may be compiled into NAMD for better PME performance.
- X-PLOR and CHARMM are useful for setup and analysis.
- The CHARMM parameters are available for use with NAMD.
- Find CHARMM docs and forums at www.charmm.org and other useful info at http://brooks.scripps.edu/charmm_docs/charmm.htm.
- The Cornell et al. (AMBER) parameters are available in CHARMM format for use with NAMD.
- The OPLS parameters are available in CHARMM format for use with NAMD. OPLS requires the vdwGeometricSigma option, see NamdAndOPLS on the NamdWiki.
- Alchemify by Jérôme Hénin prepares files for alchemical free energy calculations.
Useful Scripts
- VMD plugins and script library
- The namdplot csh script works with Grace to plot energies, etc. (This older version uses XMGR.)
- VMD's new namdplot plugin works on Windows and has both text and graphical interfaces.
- namdstats prints average energies, etc.
- namdpstats print average on pressures for runs with outputPressure enabled.
- namddat is a hack of namdplot to write data to a file
- This front-end simplifies running NAMD and even works with our DQS setup.
- These MATLAB scripts read and write DCD trajectory files.
- Andriy Anishkin's scripts
Example Simulations
- Full examples, including structure building, are in the tutorials
- ApoA1 benchmark (92,224 atoms, periodic, PME)
config, directory, 2.8M .tar.gz, 2.7M .zip
ApoA1 has been the standard NAMD cross-platform benchmark for years.
- ATPase benchmark (327,506 atoms, periodic, PME)
config, directory, 26.9M .tar.gz, 26.9M .zip
- STMV (virus) benchmark (1,066,628 atoms, periodic, PME)
config, directory, 27.5M .tar.gz, 27.5M .zip
STMV is useful for demonstrating scaling to thousands of processors.
- tiny benchmark (507 atoms, periodic, PME)
config, directory, 33k .tar.gz, 32k .zip
This single-patch benchmark runs at about 14 ms per step and is representative of the workload of a single processor in a larger simulation. For increased parallelism (up to 8 patches) add one or more of "twoAwayX yes", "twoAwayY yes", and "twoAwayZ yes" to the config file.
- Interactive BPTI (882 atoms, small) (README, config, directory, 56k .tar.gz, 54k .zip)
- ER-GRE benchmark (36573 atoms, spherical) (config, directory, 1.1M .tar.gz, 1.0M .zip)
- decalanin (66 atoms, tiny, ancient) (config, directory, .tar.gz, .zip)
- Tcl forces (decalanin) (config, directory, .tar.gz, .zip)
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